vcfR for Whole Genome Data

Question

[jaafari.omid]

Dears all, Actually I have a generated vcf file by samtools pipeline and before doing the filtration of SNPs, I am going to check their quality, mapping and depth using vcfR. But at the first step when I want to read the vcf file I am facing with an error. Here is the command that I used:

T.vcf<- read.vcfR("species.vcf)

And here is the error I have:

Processed variant 136000Error in .read_body_gz(file, stats = stats, nrows = nrows, skip = skip, : long vectors not supported yet: memory.c:1668

I will be grateful if anybody can help me with this error.

Regards, Omid

Answer 1

[zx8754]

Use the right tool for the job, R is not great for whole genome data. Maybe use bcftools for filtering, then use R for further analysis.

[jaafari.omid]

Thanks for the answer, So you mean I can use the vcfR package for only the vcf files which are small in size? because I have used this package for a vcf file generated for GBS data but for the WGS data I have this problem.

[Kevin Blighe]

No, he means to do everything outside of R. Take a look at the functions available in BCFtools. By the way, bcftools query allows you to easily output data in tabular format, which you could then further analyse in R.